CHARMM Element doc/replica.doc 1.1#File: Replica, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Replica: Commands which deal with replication of the molecular system: Replica.# <caves>-Aug-18-1993 (Leo Caves) Initial release.# REPLICA/PATH method added by B. Brooks March 1994.# Feynmann Path Integral Methods added by B. Roux, K. Hinsen and Marc Souaille, June 1997.The commands described in this node are associated with the replication ofregions of the PSF, see *note gener:(chmdoc/struct.doc)Generate. A facilityfor replication of regions of the PSF has been implemented to support a classof methods which seek to improve the sampling of a (usually small) region ofthe molecular system, by selective replication. Such methods include LES(Locally Enhanced Sampling [Elber and Karplus 1990, J. Amer. Chem. Soc. 112,9161-9175]) and MCSS (Multiple Copy Simultaneous Search [Miranker and Karplus1991, Proteins 11, 29-34]).* Menu:* Syntax:: Syntax of the replication commands* Usage:: Description of command usage* Implementation:: A brief description of the anatomy of replication * Restrictions:: Restrictions on usage* Examples:: Supplementary examples of the use of REPLica* Path:: Replica Path Method* Pathint:: Path Integral Calculation using REPLica#File: Replica, Node: Syntax, Up: Top, Next: Usage, Previous: TopSyntax of PSF Replication commands[SYNTAX: REPLication commands]REPLica { [segid] [NREPlica integer] [SETUP] [atom-selection] [COMP] } { RESEt }segid:== Basename for replica segment identifiers. atom-selection:== (see *note select:(chmdoc/select.doc).) { OFF }RPATh { [KRMS real] [KANGle real] [COSMax real] [MASS] [WEIGht] other-spec}other-spac:== [ KMIN real RMIN real ] [ KMAX real RMAX real ] [ EVWIdth real ] [ CYCLic ] [ROTAte ] [TRANslate ] [NOROtate] [NOTRanslate]#File: Replica, Node: Usage, Up: Top, Next: Implementation, Previous: SyntaxDescription of REPLica command usage1) (The implicit GENERate subcommand)This command performs the essential act of replication. Its action is toreplicate (to a degree specified by NREPlica, default: 2) (a subset of) themolecular system, as specified in the (primary) atom-selection (default: all).All atomic properties and topological attributes of the region are replicated(for a full list, see *note implem:(chmdoc/replica.doc)Implementation). Eachreplica of the primary atom selection constitutes a new segment in (and appended to) the PSF, however the atom and residue names and the residueidentifiers of the primary atom selection are carried over.The implicit generation subcommand optionally accepts a segment identifier(segid). The length of segid must be such that when concatenated with the(integer representing the) maximum number of replicas specified for generation,it does not exceed 4 characters. If omitted, then replica segment identifierswill simply be set to the replica number. At present no check is made forduplicate segment identifiers, so choose with care. The command is designed tooperate in a manner similar to the GENErate command from the main parser.The effect of the replication command may be classified into two areas:structure and interactions. Structurally, as mentioned above, the commandperforms the necessary book-keeping work for CHARMM, in order that eachindividual replica is functionally equivalent to the region of the structurespecified in the atom selection. ie. in the case where the atomic positions ofan individual replica are the same as the primary atom selection (as they willbe immediately after issuing the REPLica command), the energy and forces of theindividual replica and the appropriate region of the primary system areidentical (there is an important corollary to this statement which is nowdiscussed).In the area of discussing the interactions of replicas it is useful tointroduce the concept of a subsystem. Before issuing a REPLica command, thereis considered to be one subsystem, the primary subsystem, to which all atomsbelong. Upon issuing the REPLIca command a new subsystem is generated, whichconsists of replicas of a subset of the primary subsystem (as specified in theatom selection). In this case there are now two subsystems.The simple cases specifying interactions of subsystems and replicas may nowbe stated:* Replicas within a subsystem do NOT interact. * Replicas belonging to different subsystems do interact. In CHARMM, the interaction rules of replicas are applied in the non-bonded listgeneration routines, through appropriate group/atom exclusions. You will noticesome diagnostic messages from the list generation routines indicating thenumber of group/atom interactions excluded on the basis of replication. Infollowing the rules of interaction of replicas it is important to note that agiven replication of a subset of the primary subsystem, results in a newsubsystem. Thus the subset of the primary subsystem and its individual replicasare now in different subsystems and are thus will interact. For this reason,the replication action is usually followed by an immediate removal of the atomsof the subset of the primary subsystem, through a call to DELEte *notedele:(chmdoc/struct.doc)Delete). This leaves all replicas of the specifiedregion in a single subsystem, arranged as contiguous segments appended to thecurrent PSF.A note on renormalization of energy and forces:In the original implementation of REPLica in a developmental version of CHARMMat Harvard, there exists a close coupling of the REPLica command and theenergy/force evaluation routines. In the current REPLica implementation in thestandard CHARMM distribution, appropriate energy/force scaling for the systemin question may be achieved through the use of the BLOCK facility of CHARMM see*note Block(chmdoc/block.doc). The combination of REPLica and BLOCK providesfor very flexible method of handling replica interactions. Note that if theprimary system is FIXed and that only one replicated subsystem is present (thecase in many MCSS applications) then normalization of energy/forces is NOTrequired.Example:In the following section of CHARMM command script, a segment named PROT isgenerated from a sequence read from a coordinate file. A couple of selectiondefinitions are made which together identify the sidechain atoms of